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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.140463361812942

Latest revision as of 11:26, 17 September 2013


Full id: C612_Neutrophils_Eosinophils_granulocyte_CD14_CD4_acute_CD19



Phase1 CAGE Peaks

Hg19::chr10:114206956..114207040,+p1@VTI1A
Hg19::chr10:30024802..30024871,-p5@SVIL
Hg19::chr12:116715340..116715396,-p2@MED13L
Hg19::chr12:116715402..116715427,-p3@MED13L
Hg19::chr13:28712614..28712703,+p2@PAN3
Hg19::chr14:51297837..51297887,-p1@NIN
Hg19::chr17:4046257..4046349,-p1@ZZEF1
Hg19::chr17:63052873..63052927,-p2@GNA13
Hg19::chr1:16174280..16174365,+p1@SPEN
Hg19::chr20:20693269..20693316,-p1@RALGAPA2
Hg19::chr22:24059505..24059562,-p1@GUSBP11
Hg19::chr3:57678772..57678838,-p1@FAM116A
Hg19::chr6:79787593..79787644,-p@chr6:79787593..79787644
-
Hg19::chr7:152133059..152133102,-p1@MLL3


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
leukocyte9.07e-47136
hematopoietic stem cell4.66e-46168
angioblastic mesenchymal cell4.66e-46168
hematopoietic oligopotent progenitor cell5.60e-42161
hematopoietic multipotent progenitor cell5.60e-42161
hematopoietic cell8.09e-41177
hematopoietic lineage restricted progenitor cell1.81e-36120
nongranular leukocyte2.39e-35115
myeloid leukocyte3.81e-2872
myeloid cell4.14e-28108
common myeloid progenitor4.14e-28108
granulocyte monocyte progenitor cell8.05e-2567
myeloid lineage restricted progenitor cell1.26e-2266
macrophage dendritic cell progenitor2.42e-2261
monopoietic cell2.95e-2159
monocyte2.95e-2159
monoblast2.95e-2159
promonocyte2.95e-2159
classical monocyte5.37e-2142
CD14-positive, CD16-negative classical monocyte5.37e-2142
defensive cell2.47e-2048
phagocyte2.47e-2048
lymphoid lineage restricted progenitor cell1.47e-1252
lymphocyte2.44e-1253
common lymphoid progenitor2.44e-1253
nucleate cell4.33e-1255
mature alpha-beta T cell3.46e-0918
alpha-beta T cell3.46e-0918
immature T cell3.46e-0918
mature T cell3.46e-0918
immature alpha-beta T cell3.46e-0918
T cell1.73e-0725
pro-T cell1.73e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.36e-2798
blood island1.36e-2798
hemolymphoid system6.28e-25108
adult organism8.00e-22114
bone marrow4.15e-1976
immune system6.22e-1993
bone element2.54e-1882
skeletal element1.31e-1390
skeletal system2.84e-11100
blood2.19e-0715
haemolymphatic fluid2.19e-0715
organism substance2.19e-0715
neural tube3.22e-0756
neural rod3.22e-0756
future spinal cord3.22e-0756
neural keel3.22e-0756


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.14.74621
MA0004.11.38635
MA0006.10.906232
MA0007.10.260673
MA0009.10.695988
MA0014.15.6546
MA0017.10.181071
MA0019.10.403106
MA0024.11.45408
MA0025.10.824398
MA0027.12.28954
MA0028.10.953983
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.11.58526
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.11.9654
MA0056.10
MA0057.14.2687
MA0058.12.44274
MA0059.10.199079
MA0060.10.266757
MA0061.10.0626878
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.11.49957
MA0069.10.681911
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.14.87356
MA0074.10.358953
MA0076.11.14644
MA0077.10.65962
MA0078.10.447828
MA0081.10.578007
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.11.82993
MA0089.10
MA0090.10.223576
MA0091.10.278153
MA0092.10.247341
MA0093.12.10399
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.146091
MA0105.10.225264
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.660878
MA0113.10.414278
MA0114.10.104181
MA0115.10.929032
MA0116.10.354243
MA0117.10.732
MA0119.10.548507
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.11.17298
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.12.22701
MA0140.10.873545
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.11.08559
MA0145.10.324645
MA0146.12.95934
MA0147.10.72854
MA0148.10.296708
MA0149.12.345
MA0062.21.2433
MA0035.20.326883
MA0039.23.08805
MA0138.21.13988
MA0002.20.248488
MA0137.20.504333
MA0104.21.42323
MA0047.20.388882
MA0112.20.150022
MA0065.20.846317
MA0150.10.624926
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.0872435
MA0155.10.744296
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.15.53451
MA0163.15.26019
MA0164.10.425415
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.218.6616
MA0102.21.22472
MA0258.10.089643
MA0259.10.374338
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ATF3#46758.022562330717410.0002492312793120870.00268760615178886
CCNT2#90594.073272442333125.6650649163175e-050.000949380158529018
E2F1#1869103.505278010628095.45556518161784e-050.000924207253857235
E2F6#1876113.942050932047953.91931737261351e-060.000127556742623366
EGR1#195872.494089547405070.01176051944619070.04285613714029
ELF1#199792.737348687804850.001336570728112650.00887018556734812
HEY1#23462133.751531682883871.40950819416918e-077.98739155132038e-06
HMGN3#932484.673455841914627.53694136401289e-050.0011666675842836
JUND#372762.997713117944730.009116463920820550.0344931484051218
NFKB1#479093.528040772696040.0001816298892936060.0022016299916359
NRF1#489965.232976906161820.0005075777703933460.00444834394244447
POLR2A#5430142.147453176558072.25331953374171e-050.000492537544546777
POU2F2#545253.252187163479470.01362351556019460.0480684574861879
SIX5#14791244.881918672988290.007301455286740410.0302002648986884
SMC3#912644.298552241409380.01137870676951730.0417034235086193
TAF1#6872122.865468244924542.44753931259235e-050.000530659244898966
TBP#6908133.442001352303794.20225918943144e-072.02062498842095e-05
USF2#739265.568084593601250.0003624908317002410.00362071346326908
YY1#7528124.209574928446163.04483641911638e-071.5325285338607e-05
ZBTB7A#5134173.675954653937950.001224729241084810.00823734526079707
ZNF143#770265.786089950954810.0002939908338175250.00306979690992486



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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